Thunderbolts from mother nature brought a premature end to the second day of the first Test at Centurion Park. They arrived after thunderbolts from Mitch Johnson brought South Africa to its knees.

The Proteas' pursuit of Australia's total of 397 degenerated to near chaos - albeit not Australia-47-at-Cape-Town chaos - as the left-armer produced a spell of fast-bowling that was as hostile as anything he produced during the Ashes. He also continued his excellent form in the field with a dazzling outfield catch of J.P. Duminy, backpeddling from mid-off, that bettered his comparable catch off England's Kevin Pietersen in Perth.

Any suggestion Johnson's career-best menace was quarantined within Australian shores was shattered by him claiming three vital wickets in an opening spell, and then another late scalp to expose the home team's tail. He finished the day with 4-51 from 13 and a half overs.

When play was halted about half an hour early due to a storm South Africa was 6-140. Chief responsibility for reducing the deficit rests with vice-captain AB de Villiers. By reaching 52 not out the 29-year-old extended his record of reaching at least a half-century to 11 consecutive Tests, more than double the next best by a wicketkeeper and equal to the overall record jointly held by Viv Richards, Gautam Gambhir and Virender Sehwag.

South Africa captain Graeme Smith was a second-over victim of a fearsome Johnson delivery that he awkwardly attempted to prevent thudding into his helmet but lobbed off his bat over slips for Shaun Marsh to take a backpeddling catch. The short ball also accounted for new Proteas number-four batsman Faf du Plessis, with opener Alviro Petersen departing after a meek waft outside his off-stump that he edged behind.

Australia's advantage in the contest, after it was bowled out for 397 shortly after lunch on day two, was reinforced by Peter Siddle trapping Hashim Amla leg-before for 17, halting what had been a typically assured start to his innings.

Despite the Proteas' perilous situation de Villiers gave an early indication of why he is rated the world's best batsman in both Tests and one-dayers. This included audaciously pulling Johnson over the square-leg boundary for six just two balls after Amla departed. Duminy (5 not out) also pulled Johnson to the boundary late in the session.

Smith's positivity in scoring 10 runs off the opening over from Ryan Harris was all but forgotten because of what happened to him in the second over. He was perhaps preparing to pull Johnson, just as he had Harris' first delivery, but was so troubled by the helmet-bound trajectory of the delivery that he attempted to sway away from it but, crucially, did so without dropping his hands out of danger's way.

After he fell for 11 his partner, Peterson, joined him in Johnson's third over after a shot that reeked of carelessness. His rationale for playing such a loose shot was perhaps explained in a tweet immediately afterwards by one of the batsmen to have faced Johnson's fury of late: England's now-exiled Pietersen.

"When you facing someone as quick as Mitchell, your instinct occasionally makes you do things you shouldn't. PACE causes indecision!" Pietersen tweeted. "There is a HUGE difference when facing someone at 140kmh compared to 150kmh."

The wicket of Petersen brought Faf du Plessis to the crease, a torrid time for him to be making his first attempt at succeeding Proteas legend Jacques Kallis at number four. The right-hander lasted only five deliveries before his attempt to defend a chest-bound delivery from Johnson produced an outside edge that lobbed to delighted Australia captain Michael Clarke at second slip. At that stage the Proteas were 3-23, with Johnson having 3-10.

With Ryan Harris was not as threatening as usual the Proteas' number-three batsman, Amla, looked very comfortable, although he even looked that way against Johnson. With Siddle also looking no more than workmanlike at the start it appeared the visitors' best chance of another scalp would be when it recalled Johnson, who was excused after his four-over burst.

Siddle then made his crucial, unexpected breakthrough. His appeal from delivery that seamed into right-hander Amla beating his inside-edge and rapping him on the pad was rejected by umpire Aleem Dar. Fortunately for Australia, Siddle's plea to Clarke to review the decision was rewarded, with Dar overruled because the ball was predicted to have been on track to hit Amla's middle-stump.

The only time the Proteas halted their slide was when Duminy joined de Villiers at the crease. Their partnership, which began at 4-43, produced 67 runs. It ended at that tally after Duminy attempted to swat his second six off spinner Nathan Lyon but failed to advance enough to make it a half-volley. Johnson sprinted back from mid-off and successfully clutched the ball at full stretch, with the bowler left spreadeagled and smiling on the turf.

Clarke's decision to recall Johnson soon after Duminy's departure was rewarded with the scalp of left-hander Ryan McLaren, who lost his off-stump after being comprehensively beaten by the Australian's pace and angle into him.

Earlier, an improved day-two bowling effort by South Africa prevented Australia becoming the first touring team in four years to reach 400 in a first innings in South Africa.

The Proteas claimed Australia's last three wickets for 27 after lunch to bowl the visitors out for 397. In taking the last wicket, of Peter Siddle, Dale Steyn finished with his team's best figures: 4-78 off 29 overs.

With Australia's innings ending the last visiting team to reach 400 in a first innings remained England, which scored 9-574 at Durban in December 2009.

The key to South Africa thwarting Australia from finishing with a much larger score, after it resumed at 4-297, was keeping the stand-out batsmen of day one, Marsh (148 off 288 balls) and Steve Smith (100 off 213), to scoring only 35 more runs between them on day two.

Their fifth-wicket partnership produced 233 runs for Australia. In between their scalps vice-captain Brad Haddin was removed for a third-ball duck.

Lower-order hitting from Johnson (33) and Harris (19) ensured Australia did not fold before lunch.

The Proteas' challenge to limit the damage inflicted by Australia became even tougher when first-change seamer Morne Morkel was unable to take the field for the first 75 minutes of the day. Morkel fell on his right bowling shoulder on day one, and complained it was stiff when he woke on Thursday.

With Morkel home captain Graeme Smith had little choice but to start with Vernon Philander and Dale Steyn. Sensing the opportunities to prosper once the Proteas turned to their remaining bowlers both Marsh and Steve Smith prioritised survival for much of the first hour - rightfully so given the ball was only eight overs' old at the start of play.,

Philander and Steyn were both economical in their opening five-over spells - each claimed 0-8 - but neither was able to produce the early breakthrough their team sought. Philander thought he had Marsh caught behind on 130 after an attempted pull but the resulting review upheld umpire Dar's rejection of the appeal.

Smith began the day on 91 and by the fourth over had moved to 95, courtesy of him dispatching Steyn to the cover boundary.

He soaked up another 22 deliveries before producing stroke, a nudge into the leg-side off Peterson that brought him his third century in his past four Tests. It prompted a great reception from the Australian team balcony, just as Marsh's century had the day before.

The change from Philander and Steyn and Peterson and McLaren would ordinarily be expected to reduce the pressure on a batting team. In this instance, however, the two lesser lights gave the Proteas a belated reason to celebrate with a wicket each in consecutive overs.

Seamer McLaren looked innocuous at times on day one but started two days just as he started day one: impressively. It was him who brought the fifth-wicket partnership that spanned 422 balls to an end, when he had Smith edging off the back foot to second slip in the over after his milestone, without an addition to his score.

His replacement, Brad Haddin, lasted only three deliveries. He departed for a duck as he played over the top of a Peterson delivery he tried to sweep and was rightfully adjudged leg-before. Haddin's challenge failed after Eagle Eye predicted the ball would have slipped the top of off-stump.

Haddin's shot was particularly aggressive for a player facing only his third delivery, but given Australia's robust score and his success with such tactics in the past series in Australia it was not a totally unreasonable approach.

South Africa's morale would have been boosted by what occurred in the 109th over. The first, and clearly most significant, was Philander getting sufficient movement away from Marsh to have the left-hander fending a catch off the back foot to Graeme Smith at first slip. The second, at the end of that over, was the arrival of Morkel for the first time, and with permission to bowl him straight away because his injury was the result of an external blow.

From that point, however, Australia's tail once again demonstrated its resilience by adding without conceding a wicket in the last nine and a half overs of the session, albeit's Johnson hand was more based on aggression than resilience, scoring five boundaries.

He later gave a reminder, albeit an unnecessary one, that the aggression he could demonstrate with the bat was nothing compared to what he could do with the ball.

Scoreboard at stumps on the second day of the first Test between Australia and South Africa at SuperSport Park today: